/sci/ - Science & Math

this will keep me up at night for some time now

>>12773639
That’s not a virus. It’s a bacteriophage. They aren’t harmful to bacteria and very specific towards certain kinds of bacteria. The effects in lab are due to extrem conditions, because these extrem conditions induce phage production.
https://m.youtube.com/watch?v=MtWYQS3LFlE&feature=emb_title

>>12773639
You can think of virus as biochemical machines that occurred naturally through evolution. Same think applies to every cell in your body.

>>12773657
Bacteriophages r viruses u dumbo

>>12773670
>occurred naturally through evolution
You probably didn’t whiteness it personally.
What does naturally even mean? In the end everything has to be next to perfect to make it happen from pure chance. And even chance is just a mental construct.

>>12773639
virii are the lineage of early bacterial lifeforms that entered into a permanent endosporic phase via degenerative evolution. all aspects of a virus can be found within various bacteria, some bacteria contain all life cycle steps of a virus, but with the full bacteria existing somewhere in that cycle. some bacteria can even have full reproductive cycles without having to actually exit their endosporic forms.

one can say that they evolved to the point that they ceased to be alive, but I just consider it semantics, and in my opinion, many of the "requirements" of life are just necessities that can be stolen from something else when you need to use it.

>>12773691
>Bacteriophages r viruses
>virus
Borrowed from Latin vīrus (“poison, slime, venom”)
https://en.m.wiktionary.org/wiki/virus
Isn’t a slime. Isn’t venom and doesn’t poison bacteria. They use it to share energy and information. Phages have never been demonstrated to show any significant effect on bacteria not in extrem/metabolically stressful conditions. At least to my knowledge. So you can show the research that does support it, if it exists.

>>12773738
What a pedantic motherfucker

>>12773709
>all aspects of a virus can be found within various bacteria
That’s nice. I see you are familiar, but do you know, why that is? I give you a hint think about purification and biochemical characterization.

>>12773741
I can’t say I haven’t heard something to that effect before. I‘ve had people call me professor at the age of four.

>>12773750

it's a polite way of calling you autistic

>>12773699
>In the end everything has to be next to perfect to make it happen from pure chance.
That's the usual retarded evolution dogma, which is dying. In reality complex life emerges from any turing complete chemical soup and begins evolving immediately. The mutations are not random.

>>12773750
>call me professor at the age of four
This isn't a compliment, and the fact you have assumed it is and remembered to this day certainly reveals more about your personality than you might have thought.

>>12773757
Well. It was about me asking questions about the why too much and discussing „adult“ subjects. But you are right to some degree. To many people somebody caring about the truth basically boils down them being perceived as autistic.

>>12773765
You as a child asking 'why' is not unique or special.

>>12773764
>This isn't a compliment
Yes. It is and isn’t. I’m aware. Being intelligent is hilarious. You get all kinds of specialists from different disciplines assuming you are a colleague.

>>12773773
The amount and the topics were certainly not usual. But I think you assume my personality is more important to the conversation than it is.

>>12773783
https://www.youtube.com/watch?v=az08NU-XeHI

Damn, this kid is going to be a genius scientist and meteorologist.

>>12773786
Not going to watch it. Ad rem. Please.

>>12773709
any answer to
>>12773743

>>12773801
>Ad rem. Please.
You're autistic

>>12773639
There's no way something like that just randomly popped into existence.

I thought the consensus drifted toward viruses being alive, no?

>>12773738
>le germ theory isn’t real

Did someone not get into med school

>>12773750
You have Aspergers or some other ASD.

>>12773639
viruses came before prokaryotes, and were key in preserving ribozymes before "reverse" transcription could store rna genomes.
the entire process involves spreading enough rna to continue functioning in another lipid bubble.

>>12775352
expanding to answer the op, viruses in isolation are not metabolically active and are not alive. the key point of debate is whether requiring a host in order to do its own metabolic actions like cloning itself means it's alive or not. the stated theory says viruses are indeed alive as their rna code can complete metabolic tasks without host enzymes (ribozymes).
>>12773738
not all viruses/phages are bad sure, but bacteria create specific enzymes and pathways to remove viral data and russians have been using phage to kill (and make less virulent in cases) bacteria.
wacky 1800s medical theories don't really hold up when we can see all the active transcription going on within cells.

>>12773908
Natural selection=/=randomly popping into existence

>>12773709
>all aspects of a virus can be found within various bacteria

Find me a bacteria with RNA genome or a single-stranded DNA genome then.

>>12773639
Define "alive"

Based on your answer a virus is alive. Heck by some definitions a prion is alive.

>>12775595
There are viruses with double stranded DNA genomes. A change in storage mechanism for genetic information doesn't invalidate what they said, just means viruses evolved.

>>12773738
5 seconds on google tard

"A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy"

>>12775606
>A change in storage mechanism for genetic information doesn't invalidate what they said, just means viruses evolved.

But the fact that not even a single species of cellular life evolved to use anything else than double-stranded DNA makes me doubt that things with non-dsDNA genomes are descended from cellular life, at least of the groups that exist to this day. Maybe those RNA viruses branched off during some earlier part of life's history, before DNA appeared, who knows. Also, as far as I know, viral genes don't tend to be related to genes of cellular organisms (aside from cases of obvious gene transfer from the host to the virus and the other way round), which is pretty suspicious if they are descended from them.

>>12773763
Is this what sci has come to? People who literally don’t understand evolution?

>>12773783
Yeah sounds like your parents were cunts desu. Like a 4 year old asks many questions, making fun of of a 4 year old is lame.

>>12775244
Bacteriophages are real. It’s not a virus and phage is a misnomer.

>>12775385
Well look here
>>12713318

>>12775595
He is clueless, but correct at the same time. Here is why. We could never find a hole intact human pathogenic virus genome. Yes you heard that correctly. We could just do it for phages and giant viruses. There purification is possible. Which makes genetic and biochemical analysis of the actual thing possible. And now you get where the sequence motives of the alleged human pathogenic viruses are actually from. Despite all the failed purification attempts ex vivo. Enders started this game, when most had already give up because nothing was there. The in vitro magic started it‘s all about CPE and unscientific methodology without proper negative controls. And since you don’t have a clue, how a genome looks, if you didn’t have the particle, you need something else to do the de novo alignment. This something else always was the phages.

>>12777235
The big mystery of the viral sequence motives in front of your eyes.
But I know next to nobody will be able to believe it.
The truth is stranger than fiction.

>>12777235
>We could never find a hole intact human pathogenic virus genome. Yes you heard that correctly. We could just do it for phages and giant viruses.

15 seconds on Google:

https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239#

>>12773738
Why do we let retards like this on the internet? Christ.

>>12773765
>To many people somebody caring about the truth basically boils down them being perceived as autistic.

True.

>>12777270
Good one.
But I have terrible news for you. The human/vertebrate ones aren’t real. They are just in silico reconstructions of theoretical genomes. Electrophoresis, restriction enzymes and proper methods only occurred in phages and giant viruses.
Source every study you will find.

>>12777315
I know, you don’t even pretend to care about the scientific method or truth. But if you do, you should be glad about disagreements. Since new knowledge can be gained from the discussion and asking the deep questions.

>>12777235
>look at this meme image to justify my theory
I can admit the RNA world theory is only a hypothetical based on ribonucleotides in key vitamins and reverse transcriptase varieties, but using a meme image to refute decades of biotech research in my own field of work is pretty retarded for a fart-sniffling "genius" like yourself.
going on nearly four years ago I was in sea-phages literally isolating and sequencing lytic phage, I know that viruses don't always kill, but if you actually get your head out of your ass and look around you'd know horizontal gene transfer is just a method of genetic material keeping itself from being erased. even the sex pilus is just a plasmid meant to keep spreading between hosts and is the equivalent of bacteria herpes that gives you a dick.
a meaningful spread of info between bacteria gives ABSOLUTELY ZERO support for cell theory, and phage exists only to keep existing, no matter how it has to pick up bacterial code in order to not be chopped up.

>>12777395
>but using a meme image to refute decades of biotech research
Which meme did I use? I pointed out that killing FBS or medium starved cancer or green monkey kidney epithelium/golden hamster kidney monolayer cells with antibiotics and antimycotics and rotting impure body fluids isn’t science. Same goes for going into the whole transcriptome with primers tells you nothing.
>was in sea-phages literally isolating and sequencing lytic phage
I‘m glad you are one of the people, who knows how to isolate properly. You know this has never been done for vertebrate viruses?
>know that viruses don't always kill
Are we talking about the phages or giant viruses seen in algea for example.
>gene transfer is just a method of genetic material keeping itself from being erased
That’s just a claim.
Do you actually know, how you induce the „pathogenic“ phages in the lab?
Because I bet you do and it always boils down to extrem conditions. I have never seen halfway decent evidence of phages doing anything significant to bacteria in their natural habitat under normal conditions, which could have been interpreted as pathogenic effect on a relevant level.

>>12773639
Can we modify a virus so it injects a modified version of human dna with the intent of fixing/repairing/modify the human dna?
For example, a virus to cure down syndrome, or to trick the body to build more neural connections in the brain

>>12773738
Brainlet fuck

>>12777511
no otherwise it would be done already

>>12777526
>see someone else made the same mistake that means it’s true

>>12777537
Imagine being a brainlet

>>12777543
That’s the best you had?

>that's the best you had?

>>12777582
Oh no no no he's got a wojak reaction image, what are you gonna do anon?

>Oh no no no he's got a wojak reaction image, what are you gonna do anon?

>>12776610
what is means is that virii have evolved multiple times in life's history. virii are an incredibly complex and horribly understood branch of life with wholly novel methods of evolution.

>>12773639
that would be cool.

>>12773639
the structure of these phages is indeed quite terrifying.

>>12773657
shut up phaget

>>12777131
Turns out shitting on biology constantly results in a lot of people not knowing jack shit about the subject.

>>12777671
>hate biology
That's what happens when crazies flood the field with gaia bullshit.

>>12777664
More creative. But I think phage is also a misnomer.
>>12777131
>literally don’t understand evolution
No everybody has been thought it ad nauseam. The people, who don’t believe it probably did some thinking.
>>12777671
Biology is something very interesting. But sadly it’s has been high jacked by cultists, who think looking at dead tissue or genetically wrecked flies or mice is something meaningful.

>>12777334
30 seconds on Google for a paper on full viral genome sequencing:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122775/

>>12777589
Should have responded with a smuggie, in a proper debate they are the only argument more decisive than a basedjak

>>12777739
>thought
taught

>>12777479
>quotes meme cell theory image
>what meme did I use
the absolute state
>one of the people
it's a freshmen course made by HHMI to tell essentially highschoolers how to do actual semi-independent lab work, I did more as a tube washer in a protein lab. with vertebrate viruses, there's enough funding to image and categorize viruses by how they attack the cell down to the spike protein.
>Are we talking about the phages or giant viruses seen in algea for example.
no, I'm talking about how phage change strategies within an order of magnitude of concentration, pic related
>virus contains coding for itself and its shell
>sex pillus exists as its own transferable plasmid
(other than m.smeg, also pic related coincidently)
>the key reason why all life still exists
>just a claim

>I have never seen halfway decent evidence of phages doing anything significant to bacteria in their natural habitat under normal conditions
take dirt (don't eat it)
sample some bacteria
grow a few carpets from single colonies
now, take some more dirt, filter it through a .2 micrometer filter and dilute it down till single viral particles are in suspension
spread that over your nicely growing carpets of bacteria (choose whatever media you think is the least "stressful" for them btw, if that's what you're concerned about)
boom, wherever it dies can be sampled, repeatedly selected to be more lytic (or lysogenic) in smaller titers until you've selected a concentration you're certain came from a single virion
perfect proof of wild, native, savage, phages killing your precious bacteria without any change other than a 0.2 micron filter
then you can sequence and categorize your wild virus
so extreme, selecting for a single bacterial colony and a single phage in order to duke it out.

>>12777809
>the absolute state
Irrelevant
>actual semi-independent lab work
Yes. I know they don’t even use basic science.
>vertebrate viruses, there's enough funding to image and categorize viruses by how they attack the cell down to the spike protein.
And you know, how that’s determined? Because I bet you don’t. There is a trick involved. It’s not truly down to the spike protein.
>I'm talking about how phage change strategies within an order of magnitude of concentration
And I‘m betting on this being form a study in the laboratory under completely unusual circumstances never seen in nature. But you can show the study. I will look at it.
>key reason why all life exists
So you where there back in the begging of time to whiteness it.
>virus contains coding for itself and its shell
Thanks captain obvious.
>not just a claim
Where is the prove?
>in vitro isn’t extrem conditions for bacteria
Thanks for your expertise, but try again.

>>12777912
Also
>>12777809
>some viral particle just put it on bacterial lawn
Nothing will happen unless you select the right phage. Because they are highly specific.
>wild phage
I‘m having a good laugh with you.

>>12777912
>And you know, how that’s determined? Because I bet you don’t. There is a trick involved. It’s not truly down to the spike protein.
you know, I DO, cryoEM and crystallization were done within my university. it's truly down to the spike protein.
pic related is a simple demonstration of how we can get pics of virus dicks and confirm protein structure
>So you where(sic) there back in the begging of time to whiteness it.
the only reason why we exist right now is because a string of DNA has survived and evolved over billions of years and many generations.
viruses exist to keep their string of genes around for awhile. this IS simple shit dumbass.
proof is the fact that your own genes come from a line of many generations of animals surviving. phage survives and spreads by lytic and lysogenic processes to keep their string of code around.

>>12777955
do you need me to explain to you use diluted dirt tea to find wild viruses? really?'
you're pulling viral particles from dirt, billions of them. you take those billions and dilute them down to single particles to select and purify over multiple tirations
the entire point is to get a single (self-replicationg) particle, no one has all the time in the world to image and describe all phage.
if you want to hate in vitro methods you can get a TEM microscope and Look at single particles all day, but media is meant to create a controlled environment where we can discover how viruses and bacteria react to different situations. we want the bacteria to grow as quickly as possible, so LB works great, but when we want to see how stressed bacteria react with our virus (for classification) we choose new growth temps, media, and procedures to induce HGT, choose new food sources, and change defense mechanisms. What our professors looked for were methods to make bacteria (like botulism) change state in the presence of an isolated phage in order to stop virulence by triggering phage defence or outright killing the virulent bacteria.

>>12773639
>>what if viruses are all just malfunctioning nano machines, that use life forms to self replicate and they fell on earth eons ago?
cringe

go back to facebook

>>12778126
>you know, I DO, cryoEM and crystallization were done within my university.
Consider my mind blown. No jokes aside. I know this stuff and it never proves anything.
https://pubmed.ncbi.nlm.nih.gov/32528954/
It’s basically fishing in the dark.
The EM pictures of dying cells and the EVs and apoptotic bodies formed in the process can’t be distinguished from viruses.
>confirm protein structure
Yeah. Whatever show me the study with ex vivo purification. Because that doesn’t exist. We tried very hard with HSV-1 and ultimately failed.
>the only reason why we exist right now is because a string of DNA has survived and evolved over billions of years and many generations.
That’s just your fantasy. There is no prove and we already know it’s much more complicated than DNA.
I‘m quiet familiar with the real deal in the lab. But here for you
https://www.zeit.de/2008/25/M-Genetik/komplettansicht
It’s the basic stuff. Use the translator.
>phage survives and spreads by lytic and lysogenic processes to keep their string of code around.
I think you can’t prove it.

>>12773639
>no agreement
Everyone knows it is a force of nature, not alive.

>>12778126
>do you need me to explain to you use diluted dirt tea to find wild viruses? really?'
I would be interested, how you pull a single phage out of it.
>you're pulling viral particles from dirt, billions of them.
Okay.
>you take those billions and dilute them down to single particles to select and purify over multiple tirations
Single particles can’t be purified. You can just dilute purified particles them.
>the entire point is to get a single (self-replicationg) particle, no one has all the time in the world to image and describe all phage.
Good luck pulling a single phage out of the dirt, which is specific for a given bacteria.
>if you want to hate in vitro methods you can get a TEM microscope and Look at single particles all day, but media is meant to create a controlled environment where we can discover how viruses and bacteria react to different situations.
I don’t hate them. I just know it doesn’t really tell you much.
>we want the bacteria to grow as quickly as possible, so LB works great, but when we want to see how stressed bacteria react with our virus (for classification) we choose new growth temps, media, and procedures to induce HGT, choose new food sources, and change defense mechanisms.
Sure thing, but it’s still not the real deal.
>What our professors looked for were methods to make bacteria (like botulism) change state in the presence of an isolated phage in order to stop virulence by triggering phage defence or outright killing the virulent bacteria.
I know what’s done and it doesn’t impress me. I have never seen any good evidence for some phage nonsense working in vivo.

>>12778230
>Single particles can’t be purified
you can and you do, a single bacterial or phage colony can be collected, but in order for absolute certainty that other colonies have not overlapped you need to do the titration multiple times before sequencing
you don't waste money from getting the genome of something without repetitively making sure you didn't pick up both a lysogenic and a lytic virus, since both can infect bacteria while only one kills it in that media
its procedure meant to be certain of what you have in your vial before you send it off to be sequenced and imaged. additional titrations often show multiple phages on the 2nd collection due to the sheer variety of phage from your dirt tea, but by the 3rd are almost certainly from a single virion infecting your lawns
>Good luck pulling a single phage out of the dirt, which is specific for a given bacteria.
tons of freshmen do it every semester bud, and you can only prove if it's SPECIFIC after the fact(by running your phage against a gauntlet of other bacteria), although most are; you're just looking for phage that attacks the bacteria of interest until its pure.
>I have never seen any good evidence for some phage nonsense working in vivo.
we use lysogenic phage genes all the time to grow up protein, heck we still learn about viral vectors to make glowing worms (despite using CRISPR)
unless nematodes are not living creatures, which would be news to me considering I'm inserting shit into them right now.

I'm not debating you on in vitro shit, you're using it as an excuse to shrug off research that doesn't fit your worldview. "it was done on a pitri dish so it doesn't exist" means the only evidence I can give you are animals who have been modified using the same techniques done on a plate. there is an obvious need to make sure that research matches the real world before we give out new drugs or gene therapies, but saying all theory needs to be done from a field microscope gives a very narrow worldview.

>>12778379
>single bacterial or phage colony can be collected
>single
>colony
Well.
>the titration multiple times before sequencing
Titration is irrelevant you need some procedures like ultra centrifugation, ultra sound or French Press before anything is even close to sequencing, which you probably don’t know either.
>additional titrations often show multiple phages on the 2nd collection due to the sheer variety of phage from your dirt tea, but by the 3rd are almost certainly from a single virion infecting your lawns
Just diluting it doesn’t work.
>tons of freshmen do it every semester bud, and you can only prove if it's SPECIFIC after the fact
Tons of freshmen know it and you aren’t aware of any protocol.
>you're just looking for phage that attacks the bacteria of interest until its pure.
Link me the protocol. Because from your recollection nothing is going to be pure.

>>12778490
>>single
>>colony
>Just diluting it doesn’t work
you understand how you grow things on plates right? keyword: growth
its streaking in media in order to give space for a single viral particle to grow without influence from others
anyone who's taken microbiology has streaked a plate, streaking viruses are possible but you don't want to disturb your growing bacteria
>protocol
pic related, seems like they moved the entire manual online too https://seaphagesphagediscoveryguide.helpdocsonline.com/home
this was sooo hard to google, here's the protocol in question, although its most of chapter 5 for isolation https://seaphagesphagediscoveryguide.helpdocsonline.com/5-2-protocol

>>12778548
kek, even shit made for highschoolers holds far more info clear, demonstrable info on phage than OP

>>12778548
>naive picture of diluting supernatant
Never seen something like that.
>you understand how you grow things on plates right? keyword: growth
You are wrong. Organisms usually grow in their natural habitats.
>its streaking in media in order to give space for a single viral particle to grow without influence from others
About what „viral“ particle are you talking? You seem to be all over the place. Use the proper terminology. Why would you want to grow anything, when you can isolate it ex vivo? It’s even in your script. Your professors call it direct isolation. You need to be more open and need to ask deeper questions.

>>12778548
At least it’s a decent protocol. It’s what the vertebrate host virologists don’t do.

>>12778654
Well reading it. I think I could have come up with something better, if I had invested some time. Protein characterization is missing for example. But anybody interested can use it as a starting point look for any paper of human pathogenic viruses with this standard. It just doesn’t exist. Not that it proves phages really harm bacteria in their natural environment, but at least it shows how basics science is properly done.

>>12778633
>dilating shit is hard
>never seen it
even chem nerds know the importance of a titration (which to keep my terms in line, happens AFTER you determine concentration with your purified dilution in triplicate)
>growth plates *exist*
>explain how to isolate colonies and plaques
>you are wrong
please, educate yourself. explaining simple lab practices like a serial dilution is getting on my nerves

>angry at viral particle
its a phage particle
>use *proper* terminology
my "professor" was a bio TA in 2017, this shit is made for kids that'll spend 2-3 years playing with blocks until they start making their own protocols
the fact that you don't need a whole bunch of shit other than a filter and media is what should concern you. phage particles found in living soil is a set of dilutions away from proving viruses kill things.

It's not so much that viruses aren't alive. It's that we aren't either.

>>12778126
>>12778379
>>12778849
Kudos for raising the quality of this board, anon

>>12777511
>>12777534
brainlet here
isn't this crispr?

>>12779194
That's AAV therapy which is even older than CRISPR. The people here just don't know any bio past what they read on the first paragraph of wikipedia

>>12773750
Big man on campus fellas

>>12773709
Agreed that the whole question of whether or not viruses are living is just semantics. I mean they satisfy a lot of axioms about what constitutes "living" such as the fact that they are driven to reproduce and spread their genes just like any other terrestrial lifeform. I just wonder who even came up with the whole idea of them being non living.

>>12775606
viruses don't evolve at all really

>>12777131
one is baiting, the other trolling

>>12777131
What don't they understand? Everyone knows random mutations can't evolve shit, there's a much smarter mechanism in place. But you knew that, right anon?

>>12773765
>truth
>redefines “virus” by its linguistic origin instead of using the common scientific definition
>thinks that’s smart in any way

>>12773738
anon has brain damage

>>12777739
>No everybody has been thought it ad nauseam
You'd be surprised how many people don't actually understand it

>>12773639
What if they come from inside the body?
What if the germ theory of disease was wrong?

>>12783633
What if

>>12783694
What if I'm right? Would you care?

>>12773709
>one can say that they evolved to the point that they ceased to be alive

That sounds actually pretty cool but also extremely dark

>>12783861
what if we're all gaseous farts in a lovecraftian dream of an r34 artist?
would you care?
fact is you cant prove toxins come from within while we have bubble boy and immunoscreening

>>12773639
>what if viruses are all just malfunctioning nano machines, that use life forms to self replicate and they fell on earth eons ago?
We would have found that out by now if it were true.

>>12779841
The intuitive, common sense meaning (which is the meaning a formal, scientific definition should be based on) of the word "alive" relates to something showing agency of its own - being able to do actions from its own impulse, as opposed to being only acted on by forces in its environment.

As far as I know, viruses don't show such an "agency" - they work more like very bizarre chemicals that simply stumble upon a cell, then they undergo a series of chemical reactions (done by the cell, not by themselves), which ends in there being a bunch of copies of the original chemical.

>>12785812
Sounds like a primitive form of life to me

>>12773639
When I was taught about it 27 years ago, they had 4 criteria for the definition of life at that point; i forget exactly what the 4 were at this point, one was reproduces. Anyway, viruses met 3 of the 4 criteria as described at that time, so they told us they didn't quite qualify.

>>12773738
I am so fucking tired of schizos

>>12776610
Is this a biblically actuate angel?

>>12785812
https://youtu.be/II1R3YV1whg?t=558
your definition of life meets the colloquial definition of consciousness and being "self aware," which goes down to simple amoebas or bacteria that respond to light levels. (slime molds pretty much meet the base form of intelligence)
vague terms simply shouldn't be used and you should define what sort of "life" by key reasons. primordial life can be considered in terms of carrying out metabolism for self-replication or capability to change how it replicates (unlike prions). viruses matching a vague term doesn't change whether it can complete replication or "react" to situations.